Re: [Transdecoder-users] Does TranscriptDecoder also predict polyA?

[Brian H. <bh...@br...>]

I actually haven't researched that in a while.  Please let me know if you
find something really useful.

best,

~brian



On Sat, Jul 19, 2014 at 6:00 PM, Trakhtenberg, Feliks <
Eph...@ch...> wrote:

>  Thank you for the clarification. Any recommendations on which tool I
> could use for predicting polyA?
>
>
>  ------------------------------
> *From:* Brian Haas [bh...@br...]
> *Sent:* Saturday, July 19, 2014 5:53 PM
> *To:* Trakhtenberg, Feliks
> *Cc:* tra...@li...
> *Subject:* Re: [Transdecoder-users] Does TranscriptDecoder also predict
> polyA?
>
>   Hi,
>
>  TransDecoder does not take into account whether a transcript is
> polyadenylated or not. It strictly looks at open reading frames and coding
> potential.
>
>  best,
>
>  ~brian
>
>
>
> On Sat, Jul 19, 2014 at 2:38 PM, Trakhtenberg, Feliks <
> Eph...@ch...> wrote:
>
>>  Hello, I am new to TranscriptDecoder. Does it consider whether a novel
>> transcript with a predicted ORF is also predicted to be polyadenylated?
>> I assumed if no polyA can be predicted, then even if ORF is predicted,
>> such transcript may not produce a protein. My input is a group of novel
>> transcripts predicted by Cufflinks analysis. Would appreciate feedback.
>> thank you
>>
>>
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>
>
>  --
> --
> Brian J. Haas
> The Broad Institute
> http://broad.mit.edu/~bhaas
>
>
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas